2.0.0

⚠️ New SCILPY release 2.0.0 ⚠️

This is huge step for scilpy and our community !

This is a major refactoring of the code.
All our scripts are now organized into categories, I encourage you to check the new documentation https://scilpy.readthedocs.io/en/latest/
As always a lot of new features, unit tests and bug fixes.

Thank you to our new contributors ! 🎉
BIG thank you to all contributors especially @EmmaRenauld , @karanphil , @CHrlS98 , @AlexVCaron 🥳

See you soon 😉

What's Changed

• Volumes modules by @EmmaRenauld in #747
• Streamline operations tests by @EmmaRenauld in #762
• Create a assert_roi_radii_format function for FRF scripts by @karanphil in #771
• Connectomics module by @EmmaRenauld in #764
• Removing frf_table option by @karanphil in #772
• Move load img by @karanphil in #775
• Noddi clean up by @mdesco in #770
• Dti clean up by @mdesco in #773
• Module Gradient by @EmmaRenauld in #779
• add mti.py in reconst by @Manonedde in #768
• Asym clean up by @mdesco in #776
• fodf cleanup, deleted obselete and more by @mdesco in #788
• DWI module by @mdesco in #781
• Modify mti by @Manonedde in #786
• Support multiple input to merge (for PR in connectoflow) by @frheault in #761
• RF - changed tracking default sphere from symmetric724 to repulsion724 by @gabknight in #769
• Adding volume operations tests by @gagnonanthony in #783
• [BF] fix trk space when filter by length by @arnaudbore in #796
• Gradient sampling refactor, part2 by @EmmaRenauld in #790
• FIX: bug in scil_score_bundles.py by @AntoineTheb in #798
• [ENH] Add fix trk startrack by @arnaudbore in #797
• Fix flip startrack by @arnaudbore in #800
• Move bvec_bval_tool from utils to gradients module by @EmmaRenauld in #799
• Add test volume_math by @frheault in #778
• scil_convert_fdf.py by @arnaudbore in #801
• ENH: Adding option to skip randomization of seed. + other fixes by @EmmaRenauld in #757
• Simple framework to port scripts into legacy by @AlexVCaron in #807
• scil_merge_json move function into module by @arnaudbore in #803
• adding vtk legacy options to scil_convert_surface script by @ThoumyreStanislas in #795
• FIX/ENH: Streamline (and mask) operations refactor by @AntoineTheb in #774
• Final check main of script 1) dwi 2) gradient by @EmmaRenauld in #802
• ENH: Add Parallel Transport Tractography to scil_compute_local_tracking by @AntoineTheb in #750
• Cleaning reconst module by @karanphil in #806
• Fix round_bvals_to_shell by @karanphil in #811
• Move valid inputs from reorder_philips into module gradients by @arnaudbore in #787
• BF - metadata version when using editable install by @gabknight in #812
• Fixing scil_visualize_bundles_mosaic.py with Pillow 10.0.* by @karanphil in #814
• RF - Tracking/Tractogram Scripts by @gabknight in #815
• Legacy installation by @arnaudbore in #824
• Rename labels scripts and deprecate old by @EmmaRenauld in #819
• Rename dwi scripts by @karanphil in #823
• [Fix] Change wrong help description by @EmmaRenauld in #825
• ENH: refactor scil_compute_local_tracking by @AntoineTheb in #813
• FIX: scil_cut_streamlines now properly handles loops by @AntoineTheb in #817
• Rename connectomics and deprecate old by @EmmaRenauld in #820
• FIX import new main by @EmmaRenauld in #832
• Rename volume scripts by @arnaudbore in #829
• Rename surface scripts by @arnaudbore in #827
• Rename reconst scripts by @karanphil in #822
• Add legacy test (help) by @EmmaRenauld in #833
• Rename convert scripts by @arnaudbore in #828
• Rename reorder_dwi by @arnaudbore in #835
• Rename gradients scripts by @karanphil in #834
• [FIX] Use numbers rather than letters in scil_gradients_modify_axes by @EmmaRenauld in #821
• RF - Tractogram Scripts Renaming by @gabknight in #837
• Moving OP out of the default output files from scil_btensor_metrics.py. by @karanphil in #836
• General testing for all legacy scripts by @gabknight in #838
• Rename tractometry by @EmmaRenauld in #842
• Rename denoising by @EmmaRenauld in #847
• fix_surface_renaming by @frheault in #849
• Add throttling to jenkins pipeline by @AlexVCaron in #851
• TST - remove legacy warnings by @gabknight in #848
• RF - Scripts Renaming by @gabknight in #856
• Adding tolerance argument to fodf msmt by @karanphil in #839
• Rename some tractogram scripts by @EmmaRenauld in #846
• Rename scripts by @arnaudbore in #845
• DOC - tracking by @gabknight in #861
• [WIP] Add_verbose_arg by @ThoumyreStanislas in #850
• [WIP] Add_version_scilpy by @ThoumyreStanislas in #868
• [ENH] Add coverage by @arnaudbore in #869
• Rename small utils by @EmmaRenauld in #852
• Improved docstring and renaming by @frheault in #857
• Rename "lobe-specific metrics" to "Bingham metrics" by @CHrlS98 in #863
• Add multiple fs folder subject possibility by @arnaudbore in #844
• ENH: merge gradients convert by @AntoineTheb in #854
• Merge asymmetric filtering scripts by @CHrlS98 in #855
• Update help prompts to fit new name + add formerly: line for old script name. by @gagnonanthony in #860
• Fix basename compute dwi snr by @Manonedde in #873
• Update doc surface by @grahamlittlephd in #864
• [BF] tractoflow filter by roi by @arnaudbore in #876
• [ENH] Add pull request template by @arnaudbore in #875
• Update to dipy 1.8 by @arnaudbore in #853
• fix gdrive endpoint for tests by @AlexVCaron in #877
• Update memsmt fodf script [requires dipy 1.8.0] by @karanphil in #791
• OPT - map sh to sf before tracking [requires dipy 1.8.0] by @gabknight in #782
• Fix the script for unequal bval by @frheault in #881
• rename some scripts by @arnaudbore in #878
• Bump pillow from 10.0.1 to 10.2.0 by @dependabot in #882
• Bump pillow from 10.0.1 to 10.2.0 in /docs by @dependabot in #883
• add step to publish coverage to codecov.io by @AlexVCaron in #886
• Add Otsu threshold to scil_volume_math.py by @CHrlS98 in #887
• Fix bad commit in codecov by @AlexVCaron in #888
• Robustify the coloring by @EmmaRenauld in #890
• [WIP] Kill Jenkins by @AlexVCaron in #892
• Cancel previous concurrent build by @AlexVCaron in #893
• run workflow on PR head by @AlexVCaron in #897
• pass fetcher to DVC by @AlexVCaron in #895
• FIX: scil_visualize_connectivity text rotation by @AntoineTheb in #894
• Add perpendicular diffusivity in NODDI priors by @gagnonanthony in #872
• Adding msmt support to set_frf_diffusivities by @karanphil in #896
• Unit tests: gradients.bvec_bval_tools by @EmmaRenauld in #885
• disable test run on forks by @AlexVCaron in #899
• Fix coverage sources by @AlexVCaron in #902
• Fix coverage report paths by @AlexVCaron in #907
• Finish cleaning the main of dwi_ scripts, to allow eventual unit tests by @EmmaRenauld in #904
• Scripts to project 3D and 4D maps to streamline points and perform math operations in space of streamline points by @grahamlittlephd in #810
• Fix and uniformize verbose by @karanphil in #905
• Fix weighted mean std when infinite values by @arnaudbore in #898
• Ability to resume workflow when codecov push fails by @AlexVCaron in #909
• Fixing search keywords by @karanphil in #912
• Add gradient_utils unit tests by @EmmaRenauld in #903
• MT/ihMT scripts: cleanup and adding B1+ correction by @karanphil in #870
• Working synb0 wrapper in scilpy by @frheault in #734
• Adding tests to scil_dwi_reorder_philips.py by @karanphil in #919
• FIX: screenshot functions no longer working by @AntoineTheb in #920
• Cleaning reconst scripts part1 by @EmmaRenauld in #908
• Fix documentation by @arnaudbore in #889
• Fix Documentation - readthedoc v2 by @arnaudbore in #923
• Refactor project_streamlines_to_map by @EmmaRenauld in #911
• Unit tests dwi by @EmmaRenauld in #918
• Clarify b0 threshold by @EmmaRenauld in #867
• Add SH basis legacy support by @karanphil in #921
• Cleaning reconst scripts part2 by @EmmaRenauld in #924
• Adding msmt support and test to scil_frf_mean by @karanphil in #930
• Cleaning scil_gradients_validate_correct handling of peaks by @karanphil in #928
• Cleaning reconst scripts, part 3. by @EmmaRenauld in #926
• Bind DVC data registry by @AlexVCaron in #880
• Split load_and_verify_mti function by @karanphil in #933
• Update dvc requirements by @AlexVCaron in #938
• Reconst scripts part4 by @EmmaRenauld in #936
• [BF] Issue 932 by @arnaudbore in #934
• Unit tests for the fiber coherence by @EmmaRenauld in #929
• [ENH] Dipy 1.9 by @arnaudbore in #944
• Migrate code from aodf-toolkit by @CHrlS98 in #925
• Verify mask fit with reference in get_data_as_mask by @EmmaRenauld in #937
• Last renaming by @EmmaRenauld in #946
• New upsampling method (PTT) for tractogram by @frheault in #818
• Add description and epilog to Synthesis b0 by @frheault in #949
• Compare tractograms (TODI, TDI, ACC) by @frheault in #767
• Move utils.streamlines methods by @EmmaRenauld in #950
• Close issue 698 by @EmmaRenauld in #953
• Tractogram scripts part1 by @EmmaRenauld in #948
• Fix remove invalid overlap pts by @frheault in #955
• switch to monkeypatch.chdir by @AlexVCaron in #959
• Volumes scripts by @EmmaRenauld in #947
• Fix issue 962 by @EmmaRenauld in #963
• Tractogram scripts parts2 by @EmmaRenauld in #954
• [ENH] Add possibility to use a label mask with two values to cut streamlines by @arnaudbore in #945
• Tractogram scripts parts3 by @EmmaRenauld in #958
• Small fixes and util addition by @VincentBeaud in #965
• Updating the BundleSeg reference by @elyz081 in #964
• Forgotten renaming by @EmmaRenauld in #969
• FIX: scorer crash if only NC and --unique by @AntoineTheb in #974
• NF - add PTT options to the local tracking script by @gabknight in #976
• Unit test dpp dps management by @EmmaRenauld in #967
• Refactor visualization module by @AlexVCaron in #766
• scilpy 2.0 by @arnaudbore in #977
• Add action to publish to testpypi by @arnaudbore in #978
• BF github action by @arnaudbore in #979
• Fix install with version by @arnaudbore in #980
• BF Remove python 3.11 from install by @arnaudbore in #981

New Contributors

• @gabknight made their first contribution in #769
• @ThoumyreStanislas made their first contribution in #795
• @VincentBeaud made their first contribution in #965
• @elyz081 made their first contribution in #964

Full Changelog: 1.6.0...2.0.0